


The Secret Of the Agony Rune

by Malec24_7



Series: Malec Soulmate One shots [1]
Category: The Shadowhunter Chronicles - All Media Types
Genre: Agony Rune, Alternate Universe - Canon Divergence, Angst, Episode: s02e07 How Are Thou Fallen, Episode: s02e08 Love is a Devil, Episode: s02e09 Bound By Blood, First Time, M/M, Magnus Bane's Cat Eyes, No Smut, Self-Doubt, Self-Harm, Shadowhunters - Freeform, Soulmate-Identifying Marks, Soulmates, Warlocks
Language: English
Status: Completed
Published: 2019-07-06
Updated: 2019-07-06
Packaged: 2020-06-23 13:52:08
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 3,436
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/19702678
Author URL: https://archiveofourown.org/users/Malec24_7/pseuds/Malec24_7
Summary: Soulmate AU Following the canon of Season 2 Ep 7,8 & 9After you reach the age of 18 everyone gets their soulmate mark. This is often a symbol or depiction of something related to your soulmate.After seeing Magnus' warlock mark for the first time Alec finally realises he is Magnus' soulmate however Magnus has a rather different soulmark that couldn't possibly belong to Alec...Or could it?





	The Secret Of the Agony Rune

The important age was 18, when you reached the age of 18 you received your soulmate mark. This meant that for Magnus, he had had his soulmate mark for a very long time. Throughout his long life, he had come to understand what his mark meant and that the rune that stood strong on his shoulder meant that he would never be with his Soulmate. The agony rune. Not only was his soulmate a Shadowhunter but they were either a criminal or important member of the clave. The shadow world relations were very temperamental and he doubted that he would be finding his soulmate anytime soon despite his boyfriend’s efforts to try and unite the Nephilim and the Downworlders. Alexander. When he had first met Alexander he had at first hoped that he could be his long lost soulmate but then he realised that Alexander Gideon Lightwood would be the last person to ever use the agony rune on anyone even if he is the head of the New York Institute. Long ago he had realised he would love a great many people before and if he were ever to meet his soulmate so when he met Alec he couldn’t help but fall for him, soulmate or not. This, however, didn’t stop him from keeping his soulmark hidden from Alec. He wasn’t sure how it would sit with Alec knowing that he had another soulmate who was also a Shadowhunter. He didn’t want Alec to think there was another at all because as far as he was concerned, there wasn’t. Alec being the darling that he is had never mentioned the Soulmark before probably for the same reason he had never asked about his Warlock mark, he didn’t want to invade his space and he respected that. Magnus, therefore, had never mentioned it and never seen Alec’s mark either. He wasn’t ready to face the reality that Alec’s mark might not even be for him and for that he was also somewhat thankful. Magnus had a dangerous past and demonic influences and the last thing he wanted was for any of his impurities to taint Alec. This meant that when the night came and Magnus accidentally let his glamour drop revealing his cat eyes to Alec, he didn’t know what to say. The same Alec who told him that they were beautiful and he was beautiful and left him speechless. He wondered where that Alec was now, waking up at 8 am the next day to an empty bed and Alec’s clothes all missing. Magnus had got up and got dressed, a lot less glamorous and empty compared to his usual self, leaving his phone on silent because he was not ready for Alec to ring and break up with him because of who he really was. He had been drinking since 10 am and although he was definitely not drunk, he did feel an unusual wave of sadness pass over him that he couldn’t repress which he could of when sober. It is not often that he cried but at that moment he wasn’t sure what else he could do.

\---------

“Jace, Jace where are you, are you at the institute?” Alec begged down the phone to his brother.  
“WTF Alec, its 6 am and I’m on patrol?” He groaned into the receiver but only after he said that did he notice the excitement and nervousness in this brother’s voice, “What?”  
“I need to talk to you…In person, don’t say anything to Izzy ok?” Jace frowned  
“Is something wrong?” He panicked slightly but all he could feel through his Parabatai rune was joy.  
“No don’t worry ok, I’ll come down after patrol.”  
Jace sounded confused before he reluctantly replied, “Ok, but I won’t be back for an hour.”  
“Ok, I’ll see you at the institute.”  
Alec quietly crept back into the bedroom where he could see Magnus was still sleeping on the bed, his hair ruffled from the night before causing a blush to spread across his face. He couldn’t believe Magnus was his soulmate. He had spent all these years thinking he would never find a soulmate and that no one would ever love him like that but now he knew that the gold cat eye on his right shoulder meant Magnus was his soulmate. He had never seen Magnus’ soulmark before but he knew it must be for him somewhere. Wait what if Magnus knew it was him this whole time? Why wouldn’t he say anything? What if Magnus didn’t want him as his soulmate? Alec felt his brain rushing at 100 miles an hour. He needed to ask Jace. He would know what to do. After he had finished getting dressed he laced up his boots and swung his bow and arrows over his shoulder, leaving the loft and forgetting that leaving Magnus to wake up along was not the best idea.

\----------

When Jace saw Alec entering the institute nearly 4 hours later, he could tell his parabatai's happiness had been dulled and replaced with worry and sadness.  
“Alec, congrats for last night but please tell me you didn’t ring me at 6 am to talk about your sex life.” Alec made a horrified face before he dragged Jace into the elevator by the main entrance.  
“What Jace no! How do you even know…” Jace put his hand up laughing at the expression on his brothers face.  
“Izabelle, who do you think?” He rolled his eyes pulling a startled Alec into the quiet of his office, “Are you going to tell me what’s really going on?”  
Alec took a deep breath before unbuttoning his top 2 shirt buttons and pushing the material down below his shoulder to reveal his soulmark which he had been hiding from his family since his 18th birthday a few months ago.  
“Alec?” Jace looked at his brother’s shoulder curiously  
“It’s Magnus, Magnus is my soulmate.” He spoke aloud. The sentence sounded strangely freeing, finally, he understood what the eye really meant.  
“His warlock mark…” Jace said thoughtfully as Alec turned back around to face his Parabatai.  
“What do I do?”  
“Tell him, Alec, you idiot!” Jace said hitting his brother on the shoulder playfully.  
Doubt washed over his face, “But what if he doesn’t have my soulmark? What if I’m not his true soulmate?” Alec had clearly been overthinking as usual.  
Jace went quiet for a moment and thought about how keen Magnus had been when he met Alec for the first time. He must know. Suddenly a thought dawned on him.  
“Alec, please tell me you didn’t just up and leave Magnus this morning after everything!” Jace shouted in his face looking at his brother in shock  
Alec paled and looked completely horrified, “Oh no, What have I done.” He hurried to button up his shirt and rushed out towards the ops centre and towards the lifts.  
“Alec, did you take my advice? You did didn’t you.” Izzy stopped him before he could reach the door but before he could reply he saw his brother and Mother enter the room.  
“Mother.”

\------------

By the time Alec had managed to get back over to Magnus’ it was late morning. After being trapped by Jace, then work and his family he had finally managed to get back to the loft. When he reached the door he was nervous. He paced twice before raising his hands to knock. No answer. He knocked again, this time louder but he still got no response. Pushing down the door handle he realised the door was open. Even though Alec knew Magnus had said he could enter whenever he liked, it didn’t change the fact that he felt he was invading Magnus’ privacy.  
“Magnus?” He spoke aloud his voice carrying through the loft due to the open plan layout. He walked towards the bedroom and peeked around the door to see Magnus sitting on the window chair, looking out over Brooklyn, Martini in his hands. His face blank and eyes unfocused. At the sight of Alec, he immediately put up his glamour, gripping his cocktail tighter and whispering ‘Alexander’.  
Alec felt his heart drop into his stomach. How could he do this, make Magnus feel this way after he gave his heart to him? After they gave it to each other? Magnus was his soulmate and he had acted as if their time together meant nothing.  
“Magnus, I’m so sorry.” Alec shuffled forwards placing his hands on top of his lover’s. Magnus gripped his hands tighter turning to face Alec.  
“Don’t be ok, you have nothing to be sorry for. I’m sorry for ruining ‘your’ perfect night.” The emphasis on your made Alec’s stomach churn, the thought of Magnus feeling guilty for showing him his true self made him feel sick.  
“No, don’t say that. You didn’t ruin anything Magnus.” He moved his hands under Magnus’ chin so that he could see into his eyes. “I really like them ok?” Brushing a finger across his temples.  
“You don’t have to lie to me Alexander.” He stated pushing Alec’s hand away from his face and back down to his lap.  
“I’m not, I promise. I just had an emergency call from Jace. My mother and Max are back.” He stated facts, some being true, others not.  
Magnus looked back at his boyfriend thoughtfully, he wasn’t sure if he really believed him but Alec looked so worried and guilty that he couldn’t help but forgive him.  
“Ok, don’t worry.” He lifted his hand up to Alec’s face in a similar way to how Alec’s hand was bringing him in for a quick kiss. Alec smiled before helping Magnus into his arms. He knew Magnus still wasn’t alright but he didn’t know what to say.  
“I have something that I need to tell you…” The words were out in the open before he could stop then and Alec took a deep breath ready to confess to Magnus about the soulmark but Magnus’ eyes looking at him so expectantly prevented him from confessing.  
“It’s...it’s Max. He’s passed his final test and is ready for his rune ceremony.” Alec finally said, Magnus, looking him over suspiciously before smiling.  
“That’s great news Alexander, Is that why Jace asked you to rush over?” Magnus said quickly trying to hide the fear he has felt when Alec had started that sentence.  
“Yeah, Mum wants me to plan a party for after and I was hoping you would…” He gestured to the loft waving his hands about.  
“Alexander, I’m not sure that’s a good idea.” He looked around nervously, “I’m sure I will love max but Maryse? That woman hates me.”  
“That’s sort of the point of the party. So that she can see that this, us, is not going away.” Magnus sighed taking a deep breath.  
“Are you sure about this?”  
“Why wouldn’t I be?” Alec asked looking Magnus over. He continued to force a smile on his face before replying.  
“Well, I better get started.” Maybe a party was exactly what he needed as a distraction right now.

\---------

It had been a few hours of planning and decorating the loft when Magnus heard a shout of his name from the balcony. He was quite thankful for the party planning distraction even if it was just prolonging the time Alec was lying to him. Why didn’t he just tell him the truth this morning? He probably just didn’t want to tell Magnus he didn’t like his cat eyes.  
“Magnus!” He heard Jace shout again.  
“Salut, Mon petit chat.” He paused, walking towards Jace. “You’re new aren’t you?” He spun around filling the nearby dished with milk before moving towards Jace. “I spoil them, I can’t help it. It’s the only way to win them over.”  
Jace looked up at Magnus smiling. “I guess when you put your mind to it you can win just about anyone huh?” Jace was smiling but he looked thoughtful.  
“You’re talking about Alec.” He sighed but Jace was still looking at him smirking.  
“Well yeah, And I’m just worried about him. Especially now you have taken things to the next level.” Magnus rolled his eyes.  
“He told you?” Jace sighed moving the books to the side.  
“He didn’t have to, we’re Parabatai.” Jace looked at Magnus horrified expression before responding quickly. “No, no, It’s not like that. I can sense that he is happier.”  
“Oh, I’m not so sure about that…” Magnus sighed and Jace was confused.  
“Didn’t he tell you?” He asked surprised for a moment before putting a blank expression back onto his face.  
“Tell me what?” He eyed Jace suspiciously looking him over before deciding to reply.  
“Nothing, don’t worry.” He put his hand up to reassure Magnus however it wasn’t very effective. “I just worry about him, he’s sensitive. I’m not going to let anyone hurt him.” Jace concluded but Magnus was still eyeing him curiously.  
“I would never hurt him, we have that in common.” He responded not knowing if that was the truth. He was inevitably going to hurt him when the truth of his soulmark came up, he had already hurt Alec by showing his warlock mark, a mistake he would not make again. Putting on his usual fake smile he whispered a witty response about Maryse back to Jace but all he could think about was Alec and how he might be responsible for destroying their newfound relationship. Little did he know that there were darker things at work.

\--------

The next day, Alec and Magnus were both standing out on the balcony. The atmosphere was tense and Magnus hadn’t said anything to him about yesterday. The party or the soul sword. It had been too long since Alec had seen his happy and carefree boyfriend. Magnus had been uncharacteristically quiet over the past few days and Alec knew that it was his fault.  
“How many Downworlders to you think live in New York?” Alec broke the silence. Alec knew they couldn’t avoid what happened with Iris but he could at least try and delay the conversation.  
“I don’t know, but they’re not all your responsibility.”  
“You are.” Magnus sighed before forcing a smile on his face.  
“I can take care of myself.”  
“Maybe, but this is different,” Alec took a deep breath before carrying on, “You may have lived through the fall of Rome but even the dark ages mustn’t have seemed this dark.” He knew that maybe he was being a tad morbid but he couldn’t stop himself.  
“Alexander, I know things may seem bleak but nothing was as devastating as seeing you standing on that ledge.” Alec sighed, he knew this was coming.  
“It was the magic. I would never. Never..”  
“I know, but magic can’t create fears only bring them out.” Magnus looked Alec over and you could see that the truth was getting to him.  
“No Magnus, Don’t say anything else.” He sighed.  
“You haven’t told me anything that’s going on with you. When are you going to learn that I’m always going to be here for you even if you don’ t want me?” Alec looked confused for a moment before frustration spread across his features.  
“What? Magnus, why would you think I don’t want you?”  
“You don’t have to lie to me Alexander. I know you were disgusted by me when I revealed my warlock mark.”  
“No! Magnus. I would never think that! I’m so sorry I ran away but I promise it wasn’t because I was disgusted.” Magnus moved back towards Magnus but he backed away, face pale.  
“Do you regret that night, I am so sorry Alexander I never meant to pressure you into anything.” Magnus looked a bit horrified but Alec was quick to reassure him.  
“Magnus, no. I loved every second of it. But there’s something I need to tell you.” Magnus looked at his boyfriend nervously.  
“Whatever it is you can tell me.”  
Alec turned around and began unbuttoning his shirt. He took a deep breath and slipped it off his shoulder.  
Magnus whole face morphed into one of shock. He saw tears begin to form in Magnus’ eyes as he moved forward and ran his fingers over the small cat eye tattoo on his shoulder.  
Alec turned back around fully and saw the tears in his eyes, wrapping him into an embrace.  
“I’m sorry Magnus. I should have just told you right away rather than letting you doubt how I feel about you. Your cat eyes are beautiful and how could I not appreciate them when they are the one thing that proves you are mine.” He had now begun to cry himself and Magnus was smiling.  
“Alexander, I’m sorry I ever doubted you and I understand why you were nervous to show me.” Alec saw a shift in Magnus’ emotions from relief and happiness to worry. He reached out to place his hand on his cheek.  
“I understand and it's ok. You don’t have to show me your mark if you don’t want to. I know you have lived for a long time and have hundreds of lovers. I won't be upset if it isn’t me.” Magnus sighed before moving Alec’s hand from his cheek  
“No, I want to show you, I trust you.” Magnus mustered up the courage to remove his shirt and turned his shoulder to face Alec. He inhaled sharply before dropping his glamour.  
Alec looked horrified when he saw the Agony rune burned into Magnus’ shoulder. He could see the redness surrounding the skin suggesting it must be quite painful.  
“By the Angel, Doesn’t it hurt?” He said moving forward and running his fingers over the rune. He could see Magnus’ body shaking, his shoulders hunched.  
“Hey? Magnus, it's ok.” He spun him back around and looked into his eyes. His glamour was dropped and he was trying to hide again.  
“I’m sorry Alexander, I didn’t want to know that my soulmate was another Shadowhunter. I didn’t want you to want me any less.” Alec brought Magnus into a hug and let a few of his own tears escape.  
“It’s not a different Shadowhunter.” Alec whispered into his ear very softly, not having the courage to speak aloud.  
Magnus pushed Alec back out from his shoulder placing both his hands on Alec’s shoulders.  
“What do you mean?”  
“I’ll explain ok, but only if you promise not to say anything while I do…” Alec spoke quietly. Magnus looked at him intently waiting for him to explain.  
“My mother always wanted me to be the perfect son. She never wanted me to follow my own dreams or do what made me happy. Everything I did was for my family and for the clave and I was ok with it. I was happy to go on without emotions because emotions cloud judgement. But even I couldn’t manage to go every day without some kind of release for my built up emotions and that’s when I tried it for the first time. All of my feelings towards Jace and compressing my emotions led to me applying the agony rune on my hip whilst using a silencing rune.”  
“Alexander…” Alec held his hand up to prevent Magnus for speaking while he finished.  
“I liked the pain. I felt like I deserved it and it felt justified, well, it did until I met you. You made me feel better, like it was ok to be myself. You encouraged me to stand up for what I believed in, to be proud of who I am. I stopped using the rune for a while but then after what happened with Joslyn It happened again…”  
“Oh Angel,” At this point, both Alec and Magnus were crying and Magnus was quick to bring Alec back into a hug, “Why didn’t you say anything, you know that I would understand. And about what happened yesterday, you don’t have to explain yourself, I’ve been through it myself. Just promise you’ll tell me if things ever get that bad. Just ring me if you ever feel like hurting yourself again because if you are hurting then I am also hurting.”  
“I promise Magnus, I’m not going anywhere. I can’t believe we are both soulmates.” Alec smiles resting his head on Magnus' shoulder.  
“I know, I never thought I would find my soulmate after all these years I thought it would be someone who hated me, for what I am but I am so happy. I care about you so much Alexander.” Alec laughed slightly before bringing Magnus into a kiss only to be disturbed by the sound of Jace and Clary entering the loft.

**Author's Note:**

> Hi Everyone, sorry for the Angsty shit. Hope it turned out ok in the end  
> Leave me a comment and let me know what you guys think! Kudos always appreciated


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